{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T20:42:14Z","timestamp":1772829734818,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Multi-parent crosses of recombinant inbred lines exist in many species for fine-scale analysis of genome structure and marker\u2013trait association. These populations encompass a wide range of crossing designs with varying potential. AlphaMPSim is a flexible simulation program that is efficiently designed for comparison of alternative designs for traits with varying genetic architectures and biallelic markers with densities up to full sequence. A large pool of founder haplotypes can be supplied by the user, or generated via integration with external coalescent simulation programs such as MaCS. From these, diverse founders for multi-parent designs can be generated automatically, and users can compare designs generated from diverse pedigrees. Full tracking of identity by descent status of alleles within the pedigree is undertaken, and output files are compatible with commonly available analysis packages in R.<\/jats:p>\n               <jats:p>Availability and implementation: Executable versions of AlphaMPSim for Mac and Linux and a user manual are available at http:\/\/www.roslin.ed.ac.uk\/john-hickey\/software-packages\/ .<\/jats:p>\n               <jats:p>Contact: \u00a0john.hickey@roslin.ed.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu206","type":"journal-article","created":{"date-parts":[[2014,5,29]],"date-time":"2014-05-29T03:33:46Z","timestamp":1401334426000},"page":"2686-2688","source":"Crossref","is-referenced-by-count":8,"title":["AlphaMPSim: flexible simulation of multi-parent crosses"],"prefix":"10.1093","volume":"30","author":[{"given":"John M.","family":"Hickey","sequence":"first","affiliation":[{"name":"1 The Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK, 2 Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. 06600 M\u00e9xico D.F. and 3 CSIRO Computational Informatics and Food Futures National Research Flagship, Dutton Park, QLD 4001, Australia"}]},{"given":"Gregor","family":"Gorjanc","sequence":"additional","affiliation":[{"name":"1 The Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK, 2 Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. 06600 M\u00e9xico D.F. and 3 CSIRO Computational Informatics and Food Futures National Research Flagship, Dutton Park, QLD 4001, Australia"}]},{"given":"Sarah","family":"Hearne","sequence":"additional","affiliation":[{"name":"1 The Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK, 2 Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. 06600 M\u00e9xico D.F. and 3 CSIRO Computational Informatics and Food Futures National Research Flagship, Dutton Park, QLD 4001, Australia"}]},{"given":"Bevan E.","family":"Huang","sequence":"additional","affiliation":[{"name":"1 The Division of Genetics and Genomics, The Roslin Institute, The University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, Scotland, UK, 2 Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Apdo. 06600 M\u00e9xico D.F. and 3 CSIRO Computational Informatics and Food Futures National Research Flagship, Dutton Park, QLD 4001, Australia"}]}],"member":"286","published-online":{"date-parts":[[2014,5,28]]},"reference":[{"key":"2023012711554165600_btu206-B1","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/1939-8433-6-11","article-title":"Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding","volume":"6","author":"Bandillo","year":"2013","journal-title":"Rice"},{"key":"2023012711554165600_btu206-B2","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1093\/bioinformatics\/btg112","article-title":"R\/qtl: QTL mapping in experimental crosses","volume":"19","author":"Broman","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012711554165600_btu206-B3","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1101\/gr.083634.108","article-title":"Fast and flexible simulation of DNA sequence data","volume":"19","author":"Chen","year":"2009","journal-title":"Genome Res."},{"key":"2023012711554165600_btu206-B4","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.1038\/ng1104-1133","article-title":"The Collaborative Cross, a community resource for the genetic analysis of complex traits","volume":"36","author":"Complex Trait Consortium","year":"2004","journal-title":"Nat. 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